GEO DataSets

(Submitter supplied) DNA methylation is tightly linked with gene expression regulation and has long been regarded a stable epigenetic mark in postmitotic cells. However, it recently became clear that postnatal brains appear to show stimulus-induced de novo CpG methylation or active demethylation related to neuronal plasticity. Due to striking homologies between the brains of birds and mammals, songbirds, especially the zebra finch, propose an attractive model for investigating the genome-wide DNA methylation profile and DNA methylation reconfiguration during brain development. more...

Organism:

Taeniopygia guttata

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL19155

10 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) DNA methylation analysis of 68 glioblastoma specimen of patients treated within clinical trials, 5 samples of normal brain tissue (non-tumor brain) and 4 tumor-derived glioma sphere lines. The data was used to identify changes in DNA methylation which contribute to the aberrant of expression of HOX transcription factors. Our group had previously demonstrated that expression of HOX genes was associated with increased resistance to chemo-radiotherapy and worse outcome in GBM patients Keywords: Disease state comparison

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

77 Samples

Download data: IDAT

(Submitter supplied) DNA methylation is tightly linked with gene expression regulation and has long been regarded a stable epigenetic mark in postmitotic cells. However, it recently became clear that postnatal brains appear to show stimulus-induced de novo CpG methylation or active demethylation related to neuronal plasticity. Due to striking homologies between the brains of birds and mammals, songbirds, especially the zebra finch, propose an attractive model for investigating the genome-wide DNA methylation profile and DNA methylation reconfiguration during brain development. more...

Organism:

Taeniopygia guttata

Type:

Expression profiling by array

Platform:

GPL17605

25 Samples

Download data: CEL, TXT

(Submitter supplied) Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. more...

Organism:

Gallus gallus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9385

2 Samples

Download data: TXT

(Submitter supplied) 61 human HCCs were analyzed for genome-wide gene expression. Samples were collected at two sites in Germany, Heidelberg (HD) and Hannover (N). The Heidelberg Collection include 40 independent HCC: 19 liver resections and 17 explant liver specimen (4 not determined); median age at surgery was 57 years (range, 16-78), and the male/female ratio was 3:1. All diagnoses were confirmed by histological reevaluation, and use of the samples was approved by the local ethics committee. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

80 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of normal adrenocortical tissue, adrenocortical adenomas and adrenocortical carcinomas. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles. Samples included 6 normal adrenocortical tissue samples, 27 adenomas and 15 carcinomas.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

48 Samples

Download data: TXT

(Submitter supplied) Unearthing of silenced genes in colorectal cancer (CRC) is of great importance. We employed oligonucleotide microarray to find changes in global gene expression of five CRC cell lines. These were analyzed before and after treatment with the 5-aza-2'-Deoxycitidine. Expression of the responding genes was integrated with gene expression profiling generated by microarray analysis of matched colorectal tissue samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS4382 GDS4397

Platform:

GPL570

44 Samples

Download data: CEL

Analysis of colorectal cancer (CRC) cell lines treated with 5-aza-2’-deoxycytidine (5-aza-dC). 5-aza-dC, a DNA methylation inhibitor, was used to reactivate silenced genes in the CRC cell lines. Results provide insight into the molecular mechanisms underlying epigenetic alterations in CRC.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 agent, 5 cell line sets

Platform:

GPL570

Series:

GSE32323

10 Samples

Download data: CEL

Analysis of paired colorectal cancer (CRC) tumors and adjacent non-cancerous tissues. Colorectal cancer is a worldwide public health problem. Results provide insight into the molecular mechanisms underlying CRC carcinogenesis.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 17 individual, 2 tissue sets

Platform:

GPL570

Series:

GSE32323

34 Samples

Download data: CEL

(Submitter supplied) We queried a songbird brain to discover behaviorally regulated transcriptional mechanisms relevant for speech behavior. About 10% of zebra finch genes showed regulation during singing, and most were brain-region specific. We propose that the brain-regional diversity of the singing-regulated gene networks is derived both from differential combinatorial binding of transcription factors and the epigenetic state of these genes before singing begins. more...

Organism:

Taeniopygia guttata

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19155

8 Samples

Download data: BW, TXT

(Submitter supplied) Studies of transcriptional networks in multi-cellular organisms usually focus on isolated cells and typically assume that the discovered gene networks represent those present in connected cells within a complex organ like the brain. However, similar cell types connected in diverse anatomical networks could differentially influence transcriptional networks. Here, we used laser capture microdissection, expression arrays, genome mapping, and computational inference to explore behaviorally regulated gene networks in the brains of awake, behaving songbirds producing a skilled motor behavior, singing. more...

Organism:

Taeniopygia guttata

Type:

Expression profiling by array

Platform:

GPL9856

170 Samples

Download data: TXT

(Submitter supplied) Four cervical carcinoma cell lines (C4I, CaSki, HeLa, SiHa) were treated with epigenetic modifying drugs 5-aza-2’-deoxycytidine and trichostatin A. Such treatment leads to reactivation of genes that are epigenetically silenced in cancer by aberrant methylation; reactivated genes were then identified by microarray profiling. Subsets consist of 2 biological repeats and 2 dye-flip experiments for each repeat for CaSki cell line, and 3 repeats, each with 2 dye-flip experiments for C4I, HeLa, Caski cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1753

22 Samples

Download data

(Submitter supplied) To identify genes responsible for the synergistic effect of DAC with Dex, we performed cDNA microarray analyses using cDNA prepared from Dex-resistant OPM1 cells treated with/without Dex, DAC or DAC+Dex.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

4 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of human neuroglioma cell line (H4) and the Swedish double mutant-harboring H4 cell line (H4-sw). The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 2 cell lines, H4 and H4-sw.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

2 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The "rules" governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

7 Samples

Download data: CEL

(Submitter supplied) Abstract Background: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The “rules” governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor-type specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype identify pathways important as therapeutic targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

42 Samples

Download data: CEL

(Submitter supplied) Estrogen signaling and epigenetic modifications, in particular DNA methylation, are involved in regulation of gene expression in breast cancers. Here we investigated a potential regulatory cross-talk between these two pathways by identifying their common target genes and exploring potential underlying molecular mechanisms in human MCF7 breast cancer cells. Principal Findings: Gene expression profiling revealed that the expression of approximately 150 genes was influenced by both 17β-estradiol (E2) and a hypomethylating agent 5-aza-2’-deoxycytidine (DAC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13158

12 Samples

Download data: CEL, XLS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL25760

6 Samples

Download data

(Submitter supplied) MethylCap-seq was performed to characterize the genome-wide DNA methylation in CLBL-1 8.0, a doxorubicin-resistant cDLBCL cell line, and CLBL-1 as control, and aimed to investigate underlying mechanisms of doxorubicin resistance in cDLBCL. Strong difference in methylation pattern of both promoter and gene-body regions was detected between CLBL-1 8.0 and CLBL-1. Methylated peaks with fold-change greater than 4 and a P value of less than 0.01 were defined as differentially methylated regions (DMRs); there were a total of 20289 hypermethylated and 38362 hypomethylated DMRs detected. more...

Organism:

Canis lupus familiaris

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL25760

4 Samples

Download data: XLSX

(Submitter supplied) To analyze the biological relevance of methylation changes, gene expression from both CLBL-1 and CLBL-1 8.0, a doxorubicin-resistanct cDLBCL cell line, were examined. In total, we obtained 24.8 M and 23.7 M sequence reads for CLBL-1 and CLBL-1 8.0, respectively. After filtering out low-quality bases and reads from the datasets prior to read mapping, 19.8 M reads for CLBL-1 and 19.1 M reads for CLBL-1 8.0 were mapped to canine genome. more...

Organism:

Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25760

2 Samples

Download data: XLSX